miRNA: 3'- cGGUGGUGU-GAGuauCGGuG-GCGCCG- -5'
miRNA: 3'- -CGGUGGUGu------GAgUAUCGG------------UGGCGCCG- -5'
miRNA: 3'- cGGUGGUGUGaguauCGG-UGGCGCCG- -5'
miRNA: 3'- -CGGUGGUGUGAGUAUCGGUGGCGCCG- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 29699 | 3' | -56.8 | NC_006269.1 | + | 3852 | 0.66 | 0.153765 |
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Target: 5'- aCCACCACAgCUCuu-GUCcCgCGCGGUu -3' miRNA: 3'- cGGUGGUGU-GAGuauCGGuG-GCGCCG- -5' |
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| 29699 | 3' | -56.8 | NC_006269.1 | + | 4263 | 0.73 | 0.042569 |
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Target: 5'- cGUCACCACcuguagcCUgGUAGCCacggccuuaaaaGCCGCGGUg -3' miRNA: 3'- -CGGUGGUGu------GAgUAUCGG------------UGGCGCCG- -5' |
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| 29699 | 3' | -56.8 | NC_006269.1 | + | 2276 | 0.75 | 0.02933 |
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Target: 5'- aCCACCACACgacu-GUCuGCCGCGGCc -3' miRNA: 3'- cGGUGGUGUGaguauCGG-UGGCGCCG- -5' |
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| 29699 | 3' | -56.8 | NC_006269.1 | + | 4193 | 1.13 | 1.6e-05 |
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Target: 5'- uGCCACCACACUCAUAGCCACCGCGGCu -3' miRNA: 3'- -CGGUGGUGUGAGUAUCGGUGGCGCCG- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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